ebanks 44f3c5639a I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such... ... We can now emit bzipped VCFs from the GATK. Details: any walker that defines a VCFWriter for its @Output (i.e. pretty much every core walker from UG and on), also has associated with it the -bzip (--bzip_compression) boolean argument. When set, it will emit a VCF that is compressed with bzip2. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4093 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-24 04:14:50 +00:00
..
storage	I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...	2010-08-24 04:14:50 +00:00
stubs	I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...	2010-08-24 04:14:50 +00:00
CompressedVCFWriter.java	I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...	2010-08-24 04:14:50 +00:00
DirectOutputTracker.java	Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem.	2009-09-15 21:06:45 +00:00
OutputTracker.java	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
StingSAMFileWriter.java	Enhance the I/O management system to support custom headers and set the presorted flag	2010-01-12 18:21:42 +00:00
ThreadLocalOutputTracker.java	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00